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IMGT/PRIMER-DB


NAR Molecular Biology Database Collection entry number 505
Folch, G., Ehrenman, F. and Lefranc, M.-P.
Université Montpellier 2, CNRS, Montpellier, France.

Database Description

IMGT/PRIMER-DB is the IMGT® oligonucleotide (primer) database for the immunoglobulins (IG) and T cell receptors (TR). The IG and TR primers are useful for combinatorial library constructions, antibody single chain Fragment variable (scFv), phage display or microarray technologies. IMGT/PRIMER-DB is part of IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org (1,2), the high-quality integrated knowledge resource specialized in IG, TR, major histocompatibility complex (MHC) of human and other vertebrate species, and related proteins of the immune system (RPI) that belong to the immunoglobulin superfamily (IgSF)and to the MHC superfamily (MhcSF). IMGT/PRIMER-DB contains information on primers and combinations of primers described as "sets" [primers sharing identical properties (species, group and orientation)] and "couples" [sets of opposite orientation for which IMGT/LIGM-DB sequences are known (or expected)]. Primers, Sets and Couples are described in IMGT Primer cards, IMGT Set cards and IMGT Couple cards, respectively. An IMGT Primer is an oligonucleotide described by comparison to an IMGT/LIGM-DB reference sequence, according to the standardized rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY axioms and concepts (3,4). Taxonomic species and IMGT classification (group, subgroup, gene, allele) of a primer are those of the IMGT/LIGM-DB reference sequence, and not those of the PCR amplification products. This provides the following advantages for data standardization: IMGT/PRIMER-DB primer definition, classification and description are independent from the experimental conditions, from DNA sources and from the different combinations (sets and couples) in which the primer can be used. This means that (i) the specificity of a primer (subgroup, gene or allele specific) which is either described experimentally or deduced from sequence comparison is not used for the primer classification, although these data are provided in the IMGT/PRIMER-DB Primer card in "Classification comments and specificity", (ii) the sequences resulting from the PCR amplifications are uniquely associated to the couples. The IMGT Primer cards are linked to IMGT/LIGM-DB flat files, IMGT Colliers de Perles and IMGT Repertoire Alignments of alleles of the IMGT/LIGM-DB reference sequence used for the primer description. IMGT/PRIMER-DB, developed by LIGM (http://www.imgt.org/textes/IMGTinformation/LIGM.html) has been on the Web since February 2002.

Recent Developments

In April 2008, IMGT/PRIMER-DB contained 1,864 entries from Homo sapiens and Mus musculus

Acknowledgements

IMGT® received funding from the European Union (EU) programmes BIOMED1 (BIOCT930038), BIOTECH2 (BIO4CT960037), 5th PCRDT (QLG2-2000-01287) and 6th PCRDT (ImmunoGrid IST-028069), from the Agence Nationale de la Recherche ANR (BIOSYS06-135457) and from the Région Languedoc-Roussillon. IMGT® is funded by the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère de la Recherche.

References

1. Lefranc, M.-P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D., and Lefranc, G. (2005) IMGT, the international ImMunoGeneTics information system®. Nucleic Acids Res., 33, D593-D597.
2. Lefranc, M.-P., Clément, O., Kaas, Q., Duprat, E., Chastellan, P., Coelho, I., Combres, K., Ginestoux, C., Giudicelli, V., Chaume, D., and Lefranc, G. (2005) IMGT-Choreography for Immunogenetics and Immunoinformatics. In Silico Biology, 5, 45-60.
3. Giudicelli, V., and Lefranc, M.-P. (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics, 15, 1047-1054.
4. Duroux, P., Kaas, Q., Brochet, X., Lane, J., Ginestoux, C., Lefranc, M.-P., and Giudicelli, V. (2008) IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie, 90, 570-583.


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